Synergistic interactions - dm_patterns
motifs_filename=/data/kreiman/databh/dm_patterns/analysis/cooc/check/dm_patterns2.50.4.3.0.38.5000.5000.5000.check-ensembl.out.txt
consensus_filename=/data/kreiman/databh/dm_patterns/analysis/dm_patterns2.dm.80.consensus.txt
transcripts_filename=/data/kreiman/databh/dm_patterns/dm_patterns2.txt
number of transcripts = 13 [n_transcripts_cl]
number of motifs = 271 [n_motifs_cl]
maximum distance (bp) = 50 [max_distance]
minimum distance factor = 0.50 [min_dist_factor]
interactions of 3 motifs [max_n_motifs]
scan threshold column = 38 [thresh_column]
seqlengths_filename = /data/kreiman/databh/dm_patterns/upstream_sequences/dm_patterns2.dm.ensembl.lengths.txt and none
motifpos_filename = /data/kreiman/databh/dm_patterns/analysis/cooc/check/dm_patterns2.50.4.3.0.38.5000.5000.5000.check-ensembl.pos-cl.txt and none
seqs_filename = /data/kreiman/databh/dm_patterns/upstream_sequences/dm_patterns2.dm.ensembl.fasta and none
robustness_filename = /data/kreiman/databh/dm_patterns/analysis/cooc/check/compare_cooc_outputs.dm_patterns2.mul.3.txt
wm_filename = /data/kreiman/databh/dm_patterns/analysis/dm_patterns2.dm.80.matlab.txt
species = dm
max_n_motifs = 3
order constraint = false
number of modules = 52 [n_cooc]
number of modules after filter = 52 [n_cooc_actual]
Click on the motif ID numbers to get further information about the motifs.
Click on n_cooc_tr_cl (the number of transcripts with non-overlapping co-occurrences within the distance and order constraints) to see a list of the transcripts and positions
Click on p_binom_sp1 to see a plot of the occurrences of the motif cluster in each transcript (Figure legend)
Summary of results
i	id1	id2	id3	consensus m1	consensus m2	consensus m3	ml1	ml2	ml3	map1	map2	map3	r_oc_sp1	r_tr_sp1	n_cooc_all	n_cooc_tr_all	n_cooc_cl	n_cooc_tr_cl	p_binom
1	8	233	264	rhhkkrwtdh	yakktakv	aayccktt	10	8	8	I_KR_01	124.29	114.762	262.29	174.86	28	24	7	4	3.30E-09
2	100	268	n	kckmrnnnaandyk	nnnyaaad	none	14	8	0	2.20732	8	n	75.84	66.4	83	79	6	5	5.80E-09
3	64	215	n	raaannrnvarar	ynncyckvkrnnannnk	none	13	17	0	8.72593	2.25513	n	163.93	144.71	32	29	5	4	8.00E-09
4	233	264	270	yakktakv	aayccktt	vamnkrrtbd	8	8	10	124.29	114.762	10	311.91	144.71	37	29	11	4	8.00E-09
5	87	267	n	kbmmaaankkc	hdaakcbb	none	11	8	0	8.52225	8	n	119.9	119.9	35	35	4	4	1.90E-08
6	64	173	n	raaannrnvarar	knsnnmnnnskcrkvnr	none	13	17	0	8.72593	9.89915	n	13.33	12.93	787	649	10	8	2.50E-08
7	95	135	n	shynhtkkccka	rntykkccavnnks	none	12	14	0	6.2064	3.37689	n	27.48	18.22	420	403	11	7	2.60E-08
8	102	243	n	tnttknnndnwnaawaa	kkkrttty	none	17	8	0	35.9758	95.1165	n	43.35	48.13	121	109	5	5	3.20E-08
9	144	201	n	rvdhkmtkckaw	vnnbnnnvkcakckr	none	12	15	0	2.70818	14.5729	n	52.46	44.08	120	119	6	5	5.00E-08
10	72	205	n	rmaaanvkcnkmnm	ynkcdknkmbynkc	none	14	14	0	10.4987	8.69747	n	85.65	87.43	49	48	4	4	7.60E-08
11	35	177	n	dkccawaaam	tdnnmhhnammaaaa	none	10	15	0	44.4408	1.84039	n	22.48	23.23	280	271	6	6	8.20E-08
12	189	220	n	kkrnnnkbkknnnknkk	rmknncrvdarnck	none	17	14	0	2.08843	2.19853	n	112.41	80.7	56	52	6	4	1.10E-07
13	178	182	n	ssnnnnnknnknnsnnknkskc	kdkckrnnndnannnnnnknbnk	none	22	23	0	19.3435	3.26998	n	33.41	37.47	157	140	5	5	1.10E-07
14	35	212	n	dkccawaaam	vaaaahnnnnnnnnnnnnvnnnnaaa	none	10	26	0	44.4408	96.7282	n	9.77	10.57	966	794	9	8	1.20E-07
15	88	192	n	kckytkkvmr	ksckbykyhkbnknbnnnk	none	10	19	0	5.34337	8.39723	n	103.2	74.94	61	56	6	4	1.50E-07
16	264	264	n	aayccktt	aayccktt	none	8	8	0	114.762	114.762	n	45.06	32.79	326	160	14	5	2.30E-07
17	68	194	n	ttnnnnwnnnnwwwnaaaw	dnkcnkscnrncra	none	19	14	0	77.8171	3.83721	n	55.22	63.59	76	66	4	4	3.00E-07
18	83	83	241	rrknkvdararnk	rrknkvdararnk	ccmtttcs	13	13	8	9.75181	9.75181	116.042	64.23	58.29	196	72	12	4	4.30E-07
19	180	258	n	vnaaannnnnnmamamd	rtaaaaar	none	17	8	0	98.7525	102.496	n	8.41	6.96	1747	1356	14	9	4.40E-07
20	113	268	n	aaarnndkraaa	nnnyaaad	none	12	8	0	0.542878	8	n	13.82	11.94	683	615	9	7	4.70E-07
21	156	201	n	kntcrywkcka	vnnbnnnvkcakckr	none	11	15	0	2.46783	14.5729	n	56.71	56.71	74	74	4	4	4.80E-07
22	146	233	n	cmaamaarmr	yakktakv	none	10	8	0	0.120609	124.29	n	26.9	27.9	195	188	5	5	5.10E-07
23	45	98	n	kkbkrkcvkc	skksnnkkkknrd	none	10	13	0	7.71919	1.48853	n	49.96	53.8	84	78	4	4	6.00E-07
24	199	208	n	srkcrrsnnnkvy	kskrknrrknkvk	none	13	13	0	6.37941	4.55535	n	31.93	24.4	230	215	7	5	1.00E-06
25	258	269	n	rtaaaaar	ntttttrnbnb	none	8	11	0	102.496	11	n	7.1	7.86	1182	1068	8	8	1.20E-06
26	233	264	n	yakktakv	aayccktt	none	8	8	0	124.29	114.762	n	90.79	42.82	104	98	9	4	1.50E-06
27	80	212	n	rnnhnkcnaaaama	vaaaahnnnnnnnnnnnnvnnnnaaa	none	14	26	0	20.0061	96.7282	n	10.78	7.56	1460	1110	15	8	1.60E-06
28	9	233	n	bvvhwaaran	yakktakv	none	10	8	0	I_HB_01	124.29	n	49.49	41.14	106	102	5	4	1.80E-06
29	95	122	n	shynhtkkccka	cdkscakbnks	none	12	11	0	6.2064	7.16415	n	20.25	21.24	259	247	5	5	2.00E-06
30	233	263	n	yakktakv	kmctrmct	none	8	8	0	124.29	85.2079	n	13.91	12.93	528	487	7	6	2.70E-06
31	10	87	n	mkaad	kbmmaaankkc	none	5	11	0	I_HSF_01	8.52225	n	13.58	12.82	618	491	8	6	2.80E-06
32	183	199	n	kssrknkssrnnk	srkcrrsnnnkvy	none	13	13	0	1.68525	6.37941	n	13.99	12.67	600	497	8	6	3.00E-06
33	170	188	n	wnnsakmkannnhk	aawthkcykb	none	14	10	0	6.50325	3.55742	n	34.68	35.56	121	118	4	4	3.30E-06
34	31	41	261	khrnkhknkwknknknndr	vakhrarhkrk	kcactcav	19	11	8	118.386	22.0843	105.574	76.77	89.93	41	35	3	3	3.60E-06
35	270	270	n	vamnkrrtbd	vamnkrrtbd	none	10	10	0	10	10	n	24.08	18.8	610	279	14	5	3.70E-06
36	264	264	270	aayccktt	aayccktt	vamnkrrtbd	8	8	10	114.762	114.762	10	54.58	34.4	346	122	18	4	3.80E-06
37	36	102	104	aawannnwnnnwwttw	tnttknnndnwnaawaa	tnnnnwnnahnnnnwwnaadnnaaw	16	17	25	44.2362	35.9758	41.6451	9.2	12.18	798	517	7	6	3.80E-06
38	247	261	n	yctstmkc	kcactcav	none	8	8	0	114.515	105.574	n	22.6	18.47	325	284	7	5	4.00E-06
39	113	231	n	aaarnndkraaa	tttttatk	none	12	8	0	0.542878	113.063	n	16.76	18.47	313	284	5	5	4.00E-06
40	44	88	n	crncrkcrrnrs	kckytkkvmr	none	12	10	0	9.94679	5.34337	n	44.02	33.31	143	126	6	4	4.30E-06
41	165	194	n	vnnkknknnnknknndnnksndnks	dnkcnkscnrncra	none	25	14	0	1.07912	3.83721	n	40.35	32.79	130	128	5	4	4.60E-06
42	233	270	n	yakktakv	vamnkrrtbd	none	8	10	0	124.29	10	n	54.15	28.74	155	146	8	4	7.80E-06
43	187	201	n	ckctkbkwdns	vnnbnnnvkcakckr	none	11	15	0	4.07677	14.5729	n	17.15	14.86	367	353	6	5	1.20E-05
44	31	83	261	khrnkhknkwknknknndr	rrknkvdararnk	kcactcav	19	13	8	118.386	9.75181	105.574	48.42	59.39	65	53	3	3	1.40E-05
45	212	241	n	vaaaahnnnnnnnnnnnnvnnnnaaa	ccmtttcs	none	26	8	0	96.7282	116.042	n	11.07	9.49	758	663	8	6	1.60E-05
46	50	181	n	wwnnnaannawwttnnnw	rnnkcnkmmrmnrc	none	18	14	0	74.5083	6.7106	n	14.4	13.73	437	382	6	5	1.70E-05
47	67	223	n	aaaawnwnnnnnwnwtnd	knsrnbrknrknkknndnnr	none	18	20	0	81.3547	15.6694	n	28.74	21.3	219	197	6	4	2.60E-05
48	110	201	n	yckckkckaw	vnnbnnnvkcakckr	none	10	15	0	2.62415	14.5729	n	22.42	18.73	234	224	5	4	4.30E-05
49	113	172	184	aaarnndkraaa	maannnmvwnnnnnnaaaw	tkbyhmaaaa	12	19	10	0.542878	101.592	0.418436	16.55	17.93	317	234	5	4	5.10E-05
50	81	227	n	kynkscakcsm	kksnknbdnnnndnnnkckks	none	11	21	0	5.18876	16.9015	n	17.49	16.99	300	247	5	4	6.30E-05
51	121	173	n	atbkccksbk	knsnnmnnnskcrkvnr	none	10	17	0	7.23416	9.89915	n	13.94	15.6	301	269	4	4	8.90E-05
52	21	21	n	srkattad	srkattad	none	8	8	0	I_BCD_01	I_BCD_01	n	12.31	13.03	682	322	8	4	0.00018
i	id1	id2	id3	consensus m1	consensus m2	consensus m3	ml1	ml2	ml3	map1	map2	map3	r_oc_sp1	r_tr_sp1	n_cooc_all	n_cooc_tr_all	n_cooc_cl	n_cooc_tr_cl	p_binom
Questions? --> kreiman@mit.edu
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